> i have simulated a 12mer DNA with water and ion. After dynamics i did
> imaging of the trajectory file and saved is as a new file. i hv given
> the script below.
>
> trajin at_traj.mdcrd
> trajout at_imgd.mdcrd
> center :1-24 mass origin
> image origin center
> center:1-5223 mass origin
> image origin center familiar
> go
>
> now when i calculate the average structure from this imaged trajectory,
> all water molecules and ion cluster around the center of DNA. I have
> gone through the previous mails on this issue but i am not get whether
> the problem can be fixed. someone kindly help me on this.
Where do you think the water and ions should be? Hint: based on the
diffusion coefficient for your given water model (in the range of 2-5
m*m/s x10**-9) how far will a given water molecule move during the course
of your simulation? Is this larger than the box size? Hint2: look at a
movie of the whole system coloring a single water differently and watch
it move. Does it stay in one place?
What you are seeing seems entirely consistent for a coordinate average
over all the atoms in the system.
\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
-/-
/-\ tec3.utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A
http://www.chpc.utah.edu/~cheatham
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jun 25 2006 - 06:07:12 PDT
